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Plant cytogenetics and cytogenomics : methods and protocols / edited by Tony Heitkam, Sònia Garcia. -- New York, NY : Humana Press, 2023. – (58.17/M592/v.2672) |
Contents
Preface
Contributors
PART I INTRODUCTION
1 Plant Cytogenetics: From Chromosomes to Cytogenomics
PART II SIZING THE NUCLEUS: METHODS FOR GENOME SIZE AND PLOIDY LEVEL ESTIMATION
2 The Use of Flow Cytometry for Estimating Genome Sizes and DNA Ploidy Levels in Plants
3 Nuclear DNA Content Estimation of Seaweed by Fluorimetry Analysis.
4 K-Mer-Based Genome Size Estimation in Theory and Practice
5 A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens
PART III GETTING TO THE CHROMOSOMES: METHODS FOR CHROMOSOME FIXATION, PREPARATION, AND MANIPULATION
6 Nitrous Oxide-Induced Metaphase Arrest: A Technique for Somatic Chromosome Analysis
7 Preparation of Mitotic Chromosomes with the Squash Technique
8 Preparation of Mitotic Chromosomes with the Dropping Technique
9 Laser Capture Microdissection: From Genomes to Chromosomes, from Complex Tissue to Single-Cell Analysis
10 Flow Cytometric Analysis and Sorting of Plant Chromosomes
PART IV PUTTING ON COLOR: BANDING AND STAINING TECHNIQUES
11 C-Banding of Plant Chromosomes
12 CMA/DAPI Banding of Plant Chromosomes
13 Silver Nitrate Staining of Nucleolar Organizer Regions (Ag-NORs) in Plant Chromosomes
14 Chromatin Immunostaining of Plant Nuclei
PART V LABELING DNA: IN SITU HYBRIDIZATION AND OTHER METHODS USING FLUORESCENT LABELS
15 Critical Steps in DAPI and FISH Imaging of Chromosome Spread Preparations
16 Formamide-Free Genomic In Situ Hybridization (ff-GISH)
17 The Use of Ribosomal DNA for Comparative Cytogenetics
18 Identification of the Sequence and the Length of Telomere DNA
19 Chromosome Painting Using Chromosome-Specific BAC Clones
20 CRISPR-FISH: A CRISPR/Cas9-Based In Situ Labeling Method
21 Preparation of Male Meiotic Chromosomes for Fluorescence In Situ Hybridization and Immunodetection with Major Focus on Dogroses
22 Extended DNA Fibers for High-Resolution Mapping
23 Visualizing Chromosome Territories and Nuclear Architecture of Large Plant Genomes Using Alien Introgressions
24 Visualization of the Nucleolus Using 5' Ethynyl Uridine
PART VI LEVERAGING DATA ONTO NUCLEI: GENOMICS-INFORMED METHODS
25 Bioinformatic Prediction of Bulked Oligonucleotide Probes for FISH Using Chorus2
26 Visualization of Oligonucleotide-Based Probes Along Pseudochromosomes Using RIdeogram, KaryoploteR, and Circlize (Circos)
27 Bulked Oligo-FISH for Chromosome Painting and Chromosome Barcoding
28 Flow Sorting-Assisted Optical Mapping
29 Chromosome Conformation Capture of Mitotic Chromosomes
30 Analysis of 5S rDNA Genomic Organization Through the RepeatExplorer2 Pipeline: A Simplified Protocol
PART VII SOFTWARE AND ONLINE PLANT CYTOGENETICS & GENOMICS RESOURCES
31 Tools for Drawing Informative Idiograms
32 Using ChromEvol to Determine the Mode of Chromosomal Evolution
33 Online Resources Useful for Plant Cytogenetics and Cytogenomics Research
Name Index
Subject Index
